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


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