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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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
molecule keywords A10F9 Fab heavy chain
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
1E6JP 3G26A 4XRQA 2M8LA 3DS0A 2M8NA 3H47A 3VRLC 4PH0A 2JYLA 4XFYA 4PH1A 4XFZA 2XT1A 2XV6A 1AUMA 5HGMA 5HGNA 4COPA 3G28A 3DS1A 5HGLA 3DS5A 2L6EA 1QRJA 1A8OA 4COCA 5JPAA 2KODA 4M0IA 3H4EA 3G0VA 1EOQA 3LRYA 3MGEA 3G1IA 4U0FA 2JYGA 3G21A 4WYMA 2JO0A 1EIAA 2BUOA 2M8PA 4XROA 4U0CA 2XXMA 3DTJA 4IPYA 2LF4A 3DS4A 4QNBA 3NTEA 1A43A 1BAJA 4U0BA 5I4TG 1D1DA 3DPHA 4U0DA 2ONTA 3DS3A 5DCKA 5HGOA 3G1GA 4U0EA 4U0AA 2EIAA 3P05A 4XFXA 3DS2A 3G29A
chains in the Genus database with same CATH superfamily
2M8NA 2MY5A 4XFYA 1RO0A 1M1KQ 3CC2P 3LRYA 2OTJP 2BUOA 1M74A 1VQOP 2LF4A 1VQPP 4XFXA 2CQ8A 2KG6A 2VSQA 2K93A 2FQ0A 3VRLC 2LKIA 2JYLA 2XZ1C 2EHTA 3RG2A 4COPA 5HGLA 3NY7B 2GZGA 2LPKA 2JO0A 2JBGA 2PY8A 1KC8Q 1N8RQ 1E0HA 2L4BA 2LIWA 1KLPA 4BPHA 3CCJP 2X2BA 2FVAA 5F2NA 2K2QA 4PXHB 3CCLP 2PEMA 1T8KA 1Q7YQ 3EJEA 4IZ6A 4XRQA 4HKGA 1VQ6P 2CGQA 4PH1A 4BPGA 3G28A 1Q86Q 3EJDA 2GDYA 3DS5A 3U43A 2N6YA 1K8AQ 2PNGA 1ZMBA 2QEXP 3DTJA 3CPWO 2GYKA 2XZ0D 1YJWP 3G1GA 3P05A 3OW2O 3E2DA 1VHNA 3CCEP 5HVCA 2KGEA 1YJ9P 1Q82Q 4F37A 1AYIA 1VQLP 3GKLC 1GXHA 4NEOA 1EIAA 5KP6B 1D1DA 3CCSP 2K0YA 3RG6C 1W2BO 2P9XA 1IUQA 4R0MA 3G26A 1RNIA 2K0XA 1QVFO 1VQ9P 5HV8A 2FADA 4M0IA 3H4EA 2N5HA 1JJ2O 1YJNP 1VQNP 1KD1Q 4U0BA 3Q20A 5I4TG 1VQMP 2QNWA 2GZIA 2MR8A 1YIJP 2JQ4A 5HGNA 5HGMA 2QA4P 5JPAA 2CG5B 3LMOA 2PEIA 2JYGA 2N50A 1K30A 5KP8B 1L0HA 3DS4A 1OR5A 5DCKA 2KWLA 1KQSO 3H47A 1QVGO 2KR5A 1CEIA 2PEJA 2FHSC 1HY8A 1L0IA 3GZMA 1M6EX 1GPJA 2AFDA 2MR7A 2K5XA 2AVAA 2MD9A 2N98A 2KORA 1S72P 3NTEA 1BAJA 2Z45A 3CMEP 2BHVA 1VQ5P 2MVVA 2KOQA 1FR2A 1E6JP 2VLPA 2LIUA 1YI2P 1GXGA 1BXIA 4COCA 1A8OA 3CCUP 1VKUA 2CNRA 1MZ8A 2GDWA 3CD6P 2K94A 5F2OA 2K0DX 1K9MQ 3G21A 2PENA 3CCQP 3HYBA 2FVFA 2WPTA 4QNBA 4PWVB 3CXCO 3DS3A 2KGAA 2Z46A 2Z44A 2KG9A 2XT1A 2XV6A 2KGCA 2M5RA 4QKOA 3DS1A 1VQKP 1NQ4A 3I56P 2LTEA 5F2KA 3MGEA 4H2WC 3WBHA 2AF8A 2L9FA 2PEQA 2KOOA 1ZNVA 4U0DA 1VQ8P 2M8LA 7CEIA 3DS0A 2MVUA 2N6ZA 1M6NA 2JGPA 4XFZA 1YITP 2EG5A 1Q81Q 4U0FA 5BS2A 3B4QA 2GZFA 2XXMA 4IPYA 2FVEA 3M1MA 3HZQA 2JAZA 1VQ7P 5HGOA 2EIAA 2L22A 4GR2A 4PH0A 2KOPA 2L6EA 3G71P 1IMPA 2N5IA 2PEKA 2E1MA 1EOQA 2DGYA 1Z6MA 3CC4P 2EFJA 4U0CA 1A43A 3I55P 2VLOA 4CA3A 2AFEA 3EJBA 1F80D 2JU1A 4DG9A 1X3OA 2OARA 1QRJA 3G0VA 1HQBA 2LMLA 2KGDA 4XROA 3G4SP 4GR6A 1UNKA 1EMVA 5EW5E 1VQ4P 4U0EA 3CCRP 5KP7B 3CCVP 5BS1A 3B5IA 3G6EP 2FACA 2MF4A 2FAEA 2DNWA 1AUMA 1NJIQ 1UJZA 2KODA 2K92A 2LL8A 2M8PA 2GDXA 2VLQA 3GJNA 2FQ1A 5CZDB 2ONTA 1RO2A 2NO8A 3GZLA 2LOLA 3CMAP 2EHSA 2KOSA 1ACPA 3H0DA 2KG8A 2CWOA 2KW2A 2FQ2A 4MRTC 4H2YC 2ROQA 1AF8A 2JB0A 4UHPB 1DV5A 5EJDA 2JU2A 3CC7P 2OTLP 2L0QA 3DS2A 3G29A 2GZJA 2PEOA 4BPFA 3CCMP 1DNYA 3G1IA 4WYMA 2GZEA 1YHQP 1K73Q 2VLNA 3DPHA 3CE7A 2ERHA 4H2XC 4U0AA 1IMQA 1M90Q
chains in the Genus database with same CATH topology
1E6JP 2M8NA 1YI2P 4XFYA 1YJ9P 1Q82Q 2OARA 1RO0A 1QRJA 1A8OA 4COCA 3CCUP 1M1KQ 3CC2P 3G0VA 3LRYA 3CD6P 5F2OA 1K9MQ 3G21A 2PENA 3CCQP 1VQLP 2OTJP 3HYBA 1EIAA 2BUOA 4XROA 1M74A 1VQOP 4QNBA 2LF4A 3G4SP 4GR6A 1D1DA 3CXCO 3DS3A 1VQ4P 4U0EA 1VQPP 4XFXA 3CCRP 3CCSP 3CCVP 3RG6C 2Z46A 5BS1A 1W2BO 2P9XA 3B5IA 1IUQA 3G6EP 3G26A 1RNIA 3VRLC 2JYLA 1QVFO 2Z44A 1VQ9P 2XT1A 1AUMA 2XV6A 1NJIQ 4COPA 3DS1A 5HGLA 1VQKP 2KODA 4M0IA 3H4EA 3I56P 5F2KA 3MGEA 1JJ2O 3WBHA 1YJNP 2JO0A 1VQNP 2M8PA 2PEQA 2PY8A 1KD1Q 4U0BA 3Q20A 5I4TG 1VQMP 4U0DA 2ONTA 1KC8Q 1N8RQ 1RO2A 1VQ8P 3CMAP 1YIJP 2M8LA 3DS0A 3H0DA 2CWOA 1M6NA 4XFZA 5HGNA 5HGMA 3CCJP 2QA4P 1YITP 5JPAA 2EG5A 1Q81Q 5F2NA 2PEIA 4U0FA 2JYGA 5BS2A 1K30A 3CCLP 2XXMA 2PEMA 4IPYA 3DS4A 3CC7P 3M1MA 3HZQA 1Q7YQ 5DCKA 5HGOA 1VQ7P 2EIAA 2OTLP 3DS2A 1KQSO 3G29A 2PEOA 4XRQA 4GR2A 3H47A 1QVGO 1VQ6P 4PH0A 2PEJA 4PH1A 3G28A 1Q86Q 1M6EX 2L6EA 3DS5A 3CCMP 3G71P 2PEKA 2E1MA 2DGYA 1EOQA 3G1IA 1K8AQ 4WYMA 1YHQP 1ZMBA 2QEXP 1K73Q 2EFJA 3CC4P 4U0CA 3DTJA 3CPWO 1S72P 3NTEA 1A43A 1BAJA 2Z45A 3I55P 3DPHA 3CMEP 1YJWP 2BHVA 3G1GA 4U0AA 1VQ5P 3P05A 3OW2O 3E2DA 1M90Q 3CCEP
chains in the Genus database with same CATH homology


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