3VRLC

Crystal structure of bmj4 p24 capsid protein in complex with a10f9 fab
Total Genus 23
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The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
23
sequence length
73
structure length
73
Chain Sequence
SILDIKQGPKESFRDYVDRFFKTLRAEQCTQDVKNWMTDTLLVQNANPDCKTILRALGPGATLEEMMTACQGV
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The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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molecule keywords A10F9 Fab heavy chain
publication title Structure of the HIV-1 capsid protein p24 in complex with the broad-spectrum antibody A10F9
rcsb
source organism Human immunodeficiency virus 1
molecule tags Immune system/viral protein
total genus 23
structure length 73
sequence length 73
chains with identical sequence D
ec nomenclature
pdb deposition date 2012-04-12

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
C PF00607 Gag_p24 gag gene protein p24 (core nucleocapsid protein)
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.1200.30 Mainly Alpha Orthogonal Bundle Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A 3vrlC00
3DS5A 3G26A 4QNBA 4PH1A 1AUMA 2LF4A 3G1GA 3P05A 4WYMA 4U0BA 1BAJA 2M8NA 4U0DA 3NTEA 4COPA 1A8OA 3LRYA 1A43A 2ONTA 4PH0A 4U0EA 3H47A 4IPYA 5I4TG 2BUOA 3VRLC 2XV6A 5HGOA 4XRQA 3G1IA 4M0IA 3DPHA 3H4EA 1EOQA 3G0VA 3DS2A 3DS1A 5DCKA 4U0CA 5HGMA 5JPAA 3DS0A 2M8LA 4XFZA 2JO0A 1QRJA 3G28A 2XT1A 3G29A 5HGLA 1D1DA 4U0AA 4XFXA 3DS3A 2JYLA 5HGNA 2EIAA 2L6EA 4U0FA 1EIAA 1E6JP 2KODA 3DS4A 3G21A 2XXMA 3DTJA 4XFYA 2M8PA 3MGEA 2JYGA 4COCA 4XROA
chains in the Genus database with same CATH superfamily
2NO8A 1YJWP 2KGAA 2M8NA 1A8OA 2GZIA 1VQ9P 5HGMA 2XT1A 2JYLA 4U0FA 2ROQA 2GZFA 2VSQA 3GZLA 1VQPP 3DS5A 2LTEA 4PH1A 2KORA 2E1MA 1VKUA 2CNRA 1VQNP 3GZMA 1UJZA 2XZ0D 3CMEP 2L4BA 4HKGA 4BPFA 1T8KA 1N8RQ 3CCLP 2KWLA 2FVFA 2LL8A 1K8AQ 4XFXA 3CCRP 3LMOA 1VQKP 4XFYA 3CCUP 2QA4P 3RG6C 5KP6B 2KOOA 4UHPB 2VLNA 1OR5A 1K30A 5CZDB 2KGCA 1KLPA 2K94A 2MR7A 3H47A 2BUOA 5HGOA 3DS1A 3CCQP 2K92A 4F37A 3CCEP 1QVFO 2KODA 2JGPA 2KGEA 3CCJP 2EG5A 1AUMA 2GZGA 2KG8A 1ZMBA 2LIUA 1M1KQ 2FQ0A 2XV6A 2ERHA 4XRQA 2DGYA 5F2OA 2FAEA 2N98A 5HGLA 2KG6A 2X2BA 2MD9A 1HY8A 1E6JP 1Q82Q 5HGNA 1M6NA 2PEIA 3Q20A 3G26A 1YHQP 3EJEA 2JQ4A 2N6ZA 1Q81Q 5HVCA 4BPGA 2KR5A 5DCKA 3OW2O 4DG9A 1FR2A 2N6YA 2JYGA 4QNBA 3EJDA 5EW5E 5I4TG 3WBHA 1VQOP 3DS0A 1M90Q 2JU1A 4U0AA 3RG2A 2JU2A 3B5IA 2GDWA 1CEIA 3CD6P 2QNWA 1YI2P 3CCSP 1BAJA 1S72P 1DV5A 2KOSA 2PEQA 2OTLP 4M0IA 3DS2A 5JPAA 1KC8Q 2FHSC 2LPKA 2Z46A 2L6EA 1M74A 3CC2P 1GXHA 2KW2A 3MGEA 1K9MQ 5EJDA 4NEOA 1VQ5P 3I56P 4MRTC 1AYIA 1QVGO 2MY5A 2FACA 3U43A 1QRJA 3CCVP 1D1DA 1ZNVA 3NY7B 1BXIA 3CC4P 5KP7B 1Z6MA 2MVUA 2JB0A 1VQ4P 2MR8A 1K73Q 2MVVA 3H4EA 1EOQA 5F2KA 2GZJA 2JO0A 1YITP 2AFEA 1EIAA 2XZ1C 1ACPA 1VQ8P 1MZ8A 1VHNA 4BPHA 2GZEA 4U0DA 1NQ4A 2CWOA 3B4QA 3CE7A 1IMQA 2FQ2A 2K0XA 1VQMP 2WPTA 4U0EA 4H2XC 1RO0A 4XFZA 3G28A 2EFJA 2K93A 3M1MA 1VQLP 3HZQA 4COCA 2AF8A 2GYKA 3H0DA 2LF4A 3P05A 5BS1A 2K2QA 2KGDA 1A43A 1KD1Q 2CQ8A 2ONTA 1YJNP 2PEJA 1X3OA 1W2BO 2OTJP 2M5RA 4CA3A 1Q86Q 3HYBA 2FADA 2JAZA 2KOQA 2MF4A 3LRYA 2N50A 2PENA 4IPYA 2PEOA 3G1IA 3GJNA 1Q7YQ 2M8LA 1YIJP 1VQ7P 1VQ6P 2EIAA 3DTJA 2FVEA 4WYMA 1M6EX 2PEMA 2K5XA 2KOPA 1GXGA 2Z44A 2GDYA 2BHVA 7CEIA 3E2DA 1UNKA 4U0CA 2L9FA 2GDXA 3G29A 2PY8A 3CMAP 2VLOA 2VLPA 3EJBA 2VLQA 2DNWA 3G4SP 1AF8A 1IMPA 2EHSA 2OARA 1NJIQ 2LMLA 3NTEA 1IUQA 1RO2A 4PXHB 2N5HA 2K0DX 3CXCO 2KG9A 2L22A 2FVAA 3G0VA 5F2NA 4R0MA 1L0IA 1YJ9P 2CGQA 3DS3A 1L0HA 3I55P 4PWVB 4IZ6A 2CG5B 3G1GA 1EMVA 4U0BA 3G71P 2K0YA 4H2YC 4QKOA 2PNGA 2FQ1A 2JBGA 1E0HA 3G6EP 4GR6A 4GR2A 2LIWA 3CCMP 3CPWO 5HV8A 2N5IA 4H2WC 2Z45A 2XXMA 2M8PA 1HQBA 2QEXP 2P9XA 2L0QA 2AFDA 4COPA 5BS2A 3CC7P 2LOLA 4PH0A 2EHTA 3VRLC 3DPHA 1GPJA 2AVAA 5KP8B 2LKIA 1JJ2O 1KQSO 3GKLC 2PEKA 1RNIA 1F80D 1DNYA 3DS4A 3G21A 4XROA
chains in the Genus database with same CATH topology
1M6NA 2PEIA 3Q20A 3G26A 1YJWP 4WYMA 1M6EX 1YHQP 3CC4P 2M8NA 1A8OA 2PEMA 1Q81Q 2Z44A 1VQ4P 1VQ9P 2BHVA 1K73Q 3E2DA 3H4EA 1EOQA 5F2KA 5DCKA 4U0CA 5HGMA 2JO0A 2XT1A 3G29A 2PY8A 3CMAP 1YITP 2JYLA 4U0FA 1EIAA 3OW2O 1VQPP 2JYGA 3DS5A 4QNBA 1VQ8P 4PH1A 3G4SP 2E1MA 2OARA 1VQNP 4U0DA 1NJIQ 3NTEA 1IUQA 2CWOA 1RO2A 1VQMP 4U0EA 3CMEP 5I4TG 3WBHA 3CXCO 5F2NA 3G0VA 1RO0A 1VQOP 1N8RQ 1YJ9P 3CCLP 3DS0A 4XFZA 3G28A 1M90Q 2EFJA 4U0AA 1K8AQ 4XFXA 3DS3A 3M1MA 3CCRP 1VQLP 3HZQA 3B5IA 1VQKP 4XFYA 3CCUP 4COCA 2QA4P 3I55P 3RG6C 3H0DA 2LF4A 3G1GA 3P05A 5BS1A 4U0BA 3G71P 3CD6P 1YI2P 3CCSP 1BAJA 1S72P 1K30A 1A43A 1KD1Q 2ONTA 3H47A 1YJNP 2BUOA 2PEJA 2PEQA 3G6EP 2OTLP 5HGOA 4GR6A 4M0IA 4GR2A 3DS2A 3DS1A 3CCQP 5JPAA 1W2BO 1KC8Q 2OTJP 3CCMP 3CPWO 3CCEP 1QVFO 2Z46A 1Q86Q 2L6EA 1M74A 3CC2P 2KODA 2Z45A 2XXMA 3HYBA 2M8PA 3MGEA 1K9MQ 3CCJP 2EG5A 2P9XA 1AUMA 2QEXP 1ZMBA 4COPA 3LRYA 1VQ5P 3I56P 5BS2A 3CC7P 4PH0A 1M1KQ 2PENA 4IPYA 3VRLC 2XV6A 2PEOA 1QVGO 4XRQA 3G1IA 3DPHA 2DGYA 5F2OA 1Q7YQ 2M8LA 1KQSO 1JJ2O 1YIJP 1QRJA 5HGLA 3CCVP 2PEKA 1VQ7P 1D1DA 1RNIA 1VQ6P 2EIAA 1E6JP 3DS4A 3G21A 3DTJA 1Q82Q 5HGNA 4XROA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3DS5 A;  3G26 A;  4QNB A;  4PH1 A;  1AUM A;  2LF4 A;  3G1G A;  3P05 A;  4WYM A;  4U0B A;  1BAJ A;  2M8N A;  4U0D A;  3NTE A;  4COP A;  1A8O A;  3LRY A;  1A43 A;  2ONT A;  4PH0 A;  4U0E A;  3H47 A;  4IPY A;  5I4T G;  2BUO A;  3VRL C;  2XV6 A;  5HGO A;  4XRQ A;  3G1I A;  4M0I A;  3DPH A;  3H4E A;  1EOQ A;  3G0V A;  3DS2 A;  3DS1 A;  5DCK A;  4U0C A;  5HGM A;  5JPA A;  3DS0 A;  2M8L A;  4XFZ A;  2JO0 A;  1QRJ A;  3G28 A;  2XT1 A;  3G29 A;  5HGL A;  1D1D A;  4U0A A;  4XFX A;  3DS3 A;  2JYL A;  5HGN A;  2EIA A;  2L6E A;  4U0F A;  1EIA A;  1E6J P;  2KOD A;  3DS4 A;  3G21 A;  2XXM A;  3DTJ A;  4XFY A;  2M8P A;  3MGE A;  2JYG A;  4COC A;  4XRO A; 
#chains in the Genus database with same CATH topology
 2NO8 A;  1YJW P;  2KGA A;  2M8N A;  1A8O A;  2GZI A;  1VQ9 P;  5HGM A;  2XT1 A;  2JYL A;  4U0F A;  2ROQ A;  2GZF A;  2VSQ A;  3GZL A;  1VQP P;  3DS5 A;  2LTE A;  4PH1 A;  2KOR A;  2E1M A;  1VKU A;  2CNR A;  1VQN P;  3GZM A;  1UJZ A;  2XZ0 D;  3CME P;  2L4B A;  4HKG A;  4BPF A;  1T8K A;  1N8R Q;  3CCL P;  2KWL A;  2FVF A;  2LL8 A;  1K8A Q;  4XFX A;  3CCR P;  3LMO A;  1VQK P;  4XFY A;  3CCU P;  2QA4 P;  3RG6 C;  5KP6 B;  2KOO A;  4UHP B;  2VLN A;  1OR5 A;  1K30 A;  5CZD B;  2KGC A;  1KLP A;  2K94 A;  2MR7 A;  3H47 A;  2BUO A;  5HGO A;  3DS1 A;  3CCQ P;  2K92 A;  4F37 A;  3CCE P;  1QVF O;  2KOD A;  2JGP A;  2KGE A;  3CCJ P;  2EG5 A;  1AUM A;  2GZG A;  2KG8 A;  1ZMB A;  2LIU A;  1M1K Q;  2FQ0 A;  2XV6 A;  2ERH A;  4XRQ A;  2DGY A;  5F2O A;  2FAE A;  2N98 A;  5HGL A;  2KG6 A;  2X2B A;  2MD9 A;  1HY8 A;  1E6J P;  1Q82 Q;  5HGN A;  1M6N A;  2PEI A;  3Q20 A;  3G26 A;  1YHQ P;  3EJE A;  2JQ4 A;  2N6Z A;  1Q81 Q;  5HVC A;  4BPG A;  2KR5 A;  5DCK A;  3OW2 O;  4DG9 A;  1FR2 A;  2N6Y A;  2JYG A;  4QNB A;  3EJD A;  5EW5 E;  5I4T G;  3WBH A;  1VQO P;  3DS0 A;  1M90 Q;  2JU1 A;  4U0A A;  3RG2 A;  2JU2 A;  3B5I A;  2GDW A;  1CEI A;  3CD6 P;  2QNW A;  1YI2 P;  3CCS P;  1BAJ A;  1S72 P;  1DV5 A;  2KOS A;  2PEQ A;  2OTL P;  4M0I A;  3DS2 A;  5JPA A;  1KC8 Q;  2FHS C;  2LPK A;  2Z46 A;  2L6E A;  1M74 A;  3CC2 P;  1GXH A;  2KW2 A;  3MGE A;  1K9M Q;  5EJD A;  4NEO A;  1VQ5 P;  3I56 P;  4MRT C;  1AYI A;  1QVG O;  2MY5 A;  2FAC A;  3U43 A;  1QRJ A;  3CCV P;  1D1D A;  1ZNV A;  3NY7 B;  1BXI A;  3CC4 P;  5KP7 B;  1Z6M A;  2MVU A;  2JB0 A;  1VQ4 P;  2MR8 A;  1K73 Q;  2MVV A;  3H4E A;  1EOQ A;  5F2K A;  2GZJ A;  2JO0 A;  1YIT P;  2AFE A;  1EIA A;  2XZ1 C;  1ACP A;  1VQ8 P;  1MZ8 A;  1VHN A;  4BPH A;  2GZE A;  4U0D A;  1NQ4 A;  2CWO A;  3B4Q A;  3CE7 A;  1IMQ A;  2FQ2 A;  2K0X A;  1VQM P;  2WPT A;  4U0E A;  4H2X C;  1RO0 A;  4XFZ A;  3G28 A;  2EFJ A;  2K93 A;  3M1M A;  1VQL P;  3HZQ A;  4COC A;  2AF8 A;  2GYK A;  3H0D A;  2LF4 A;  3P05 A;  5BS1 A;  2K2Q A;  2KGD A;  1A43 A;  1KD1 Q;  2CQ8 A;  2ONT A;  1YJN P;  2PEJ A;  1X3O A;  1W2B O;  2OTJ P;  2M5R A;  4CA3 A;  1Q86 Q;  3HYB A;  2FAD A;  2JAZ A;  2KOQ A;  2MF4 A;  3LRY A;  2N50 A;  2PEN A;  4IPY A;  2PEO A;  3G1I A;  3GJN A;  1Q7Y Q;  2M8L A;  1YIJ P;  1VQ7 P;  1VQ6 P;  2EIA A;  3DTJ A;  2FVE A;  4WYM A;  1M6E X;  2PEM A;  2K5X A;  2KOP A;  1GXG A;  2Z44 A;  2GDY A;  2BHV A;  7CEI A;  3E2D A;  1UNK A;  4U0C A;  2L9F A;  2GDX A;  3G29 A;  2PY8 A;  3CMA P;  2VLO A;  2VLP A;  3EJB A;  2VLQ A;  2DNW A;  3G4S P;  1AF8 A;  1IMP A;  2EHS A;  2OAR A;  1NJI Q;  2LML A;  3NTE A;  1IUQ A;  1RO2 A;  4PXH B;  2N5H A;  2K0D X;  3CXC O;  2KG9 A;  2L22 A;  2FVA A;  3G0V A;  5F2N A;  4R0M A;  1L0I A;  1YJ9 P;  2CGQ A;  3DS3 A;  1L0H A;  3I55 P;  4PWV B;  4IZ6 A;  2CG5 B;  3G1G A;  1EMV A;  4U0B A;  3G71 P;  2K0Y A;  4H2Y C;  4QKO A;  2PNG A;  2FQ1 A;  2JBG A;  1E0H A;  3G6E P;  4GR6 A;  4GR2 A;  2LIW A;  3CCM P;  3CPW O;  5HV8 A;  2N5I A;  4H2W C;  2Z45 A;  2XXM A;  2M8P A;  1HQB A;  2QEX P;  2P9X A;  2L0Q A;  2AFD A;  4COP A;  5BS2 A;  3CC7 P;  2LOL A;  4PH0 A;  2EHT A;  3VRL C;  3DPH A;  1GPJ A;  2AVA A;  5KP8 B;  2LKI A;  1JJ2 O;  1KQS O;  3GKL C;  2PEK A;  1RNI A;  1F80 D;  1DNY A;  3DS4 A;  3G21 A;  4XRO A; 
#chains in the Genus database with same CATH homology
 1M6N A;  2PEI A;  3Q20 A;  3G26 A;  1YJW P;  4WYM A;  1M6E X;  1YHQ P;  3CC4 P;  2M8N A;  1A8O A;  2PEM A;  1Q81 Q;  2Z44 A;  1VQ4 P;  1VQ9 P;  2BHV A;  1K73 Q;  3E2D A;  3H4E A;  1EOQ A;  5F2K A;  5DCK A;  4U0C A;  5HGM A;  2JO0 A;  2XT1 A;  3G29 A;  2PY8 A;  3CMA P;  1YIT P;  2JYL A;  4U0F A;  1EIA A;  3OW2 O;  1VQP P;  2JYG A;  3DS5 A;  4QNB A;  1VQ8 P;  4PH1 A;  3G4S P;  2E1M A;  2OAR A;  1VQN P;  4U0D A;  1NJI Q;  3NTE A;  1IUQ A;  2CWO A;  1RO2 A;  1VQM P;  4U0E A;  3CME P;  5I4T G;  3WBH A;  3CXC O;  5F2N A;  3G0V A;  1RO0 A;  1VQO P;  1N8R Q;  1YJ9 P;  3CCL P;  3DS0 A;  4XFZ A;  3G28 A;  1M90 Q;  2EFJ A;  4U0A A;  1K8A Q;  4XFX A;  3DS3 A;  3M1M A;  3CCR P;  1VQL P;  3HZQ A;  3B5I A;  1VQK P;  4XFY A;  3CCU P;  4COC A;  2QA4 P;  3I55 P;  3RG6 C;  3H0D A;  2LF4 A;  3G1G A;  3P05 A;  5BS1 A;  4U0B A;  3G71 P;  3CD6 P;  1YI2 P;  3CCS P;  1BAJ A;  1S72 P;  1K30 A;  1A43 A;  1KD1 Q;  2ONT A;  3H47 A;  1YJN P;  2BUO A;  2PEJ A;  2PEQ A;  3G6E P;  2OTL P;  5HGO A;  4GR6 A;  4M0I A;  4GR2 A;  3DS2 A;  3DS1 A;  3CCQ P;  5JPA A;  1W2B O;  1KC8 Q;  2OTJ P;  3CCM P;  3CPW O;  3CCE P;  1QVF O;  2Z46 A;  1Q86 Q;  2L6E A;  1M74 A;  3CC2 P;  2KOD A;  2Z45 A;  2XXM A;  3HYB A;  2M8P A;  3MGE A;  1K9M Q;  3CCJ P;  2EG5 A;  2P9X A;  1AUM A;  2QEX P;  1ZMB A;  4COP A;  3LRY A;  1VQ5 P;  3I56 P;  5BS2 A;  3CC7 P;  4PH0 A;  1M1K Q;  2PEN A;  4IPY A;  3VRL C;  2XV6 A;  2PEO A;  1QVG O;  4XRQ A;  3G1I A;  3DPH A;  2DGY A;  5F2O A;  1Q7Y Q;  2M8L A;  1KQS O;  1JJ2 O;  1YIJ P;  1QRJ A;  5HGL A;  3CCV P;  2PEK A;  1VQ7 P;  1D1D A;  1RNI A;  1VQ6 P;  2EIA A;  1E6J P;  3DS4 A;  3G21 A;  3DTJ A;  1Q82 Q;  5HGN A;  4XRO A; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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