3DS5 | Genus

Total Genus 28

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	28
sequence length	73
structure length	73
Chain Sequence	SILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKAWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGV

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

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

Genus data interpretation

molecule tags	Viral protein
source organism	Human immunodeficiency virus 1
publication title	Residues in the HIV-1 Capsid Assembly Inhibitor Binding Site Are Essential for Maintaining the Assembly-competent Quaternary Structure of the Capsid Protein. pubmed doi rcsb
molecule keywords	HIV-1 CAPSID PROTEIN
total genus	28
structure length	73
sequence length	73
chains with identical sequence	B, C, D
ec nomenclature	ec 2.7.7.49: RNA-directed DNA polymerase.
pdb deposition date	2008-07-11

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
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	3ds5A00

3DTJA 3DS4A 2XT1A 1EIAA 3DS2A 3NTEA 2ONTA 1QRJA 4XRQA 4PH0A 1EOQA 5HGMA 2BUOA 3G0VA 4U0CA 3G26A 4U0EA 3H47A 3DS3A 4U0FA 4U0BA 2M8LA 4XFZA 5HGOA 4PH1A 4XROA 4COPA 1A43A 2LF4A 3G29A 2M8NA 3G1GA 2XXMA 4COCA 2JYGA 3G21A 1BAJA 1A8OA 2XV6A 3G28A 5HGNA 3DS0A 3DS5A 2L6EA 3G1IA 3LRYA 4U0AA 5JPAA 1D1DA 3MGEA 4U0DA 4IPYA 2JO0A 4QNBA 2M8PA 4WYMA 3DS1A 5HGLA 2EIAA 3DPHA 3H4EA 3VRLC 1AUMA 5I4TG 2KODA 4XFYA 2JYLA 4XFXA 1E6JP 3P05A 5DCKA 4M0IA
chains in the Genus database with same CATH superfamily

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

3DTJA 1M1KQ 2ONTA 1YHQP 1YITP 3WBHA 3CCLP 2OTJP 2Z44A 4U0BA 3DS3A 1YJNP 2DGYA 3CCVP 1A43A 1VQ7P 1VQLP 1BAJA 1K73Q 4U0AA 3G1IA 3LRYA 1YI2P 3CPWO 2JO0A 4QNBA 1VQ6P 1QVFO 1VQMP 5HGLA 2EIAA 1ZMBA 3DPHA 3H4EA 4XFXA 1E6JP 2BHVA 5DCKA 2E1MA 3DS4A 1EIAA 3DS2A 3NTEA 1QRJA 2PEQA 3CCJP 5F2NA 2P9XA 5HGMA 3I55P 2BUOA 1Q7YQ 2OTLP 5HGOA 1K9MQ 1VQOP 1VQ5P 2LF4A 3E2DA 5BS1A 1KQSO 1M6NA 3G1GA 3G29A 3CCUP 1YIJP 1JJ2O 2JYGA 2XV6A 2L6EA 1D1DA 1RNIA 1RO2A 1Q81Q 4GR6A 2PEJA 1Q82Q 2PY8A 5BS2A 3H0DA 5JPAA 3CCQP 1VQ8P 2KODA 2JYLA 2XT1A 3RG6C 2PEMA 4PH0A 1EOQA 1S72P 1YJ9P 3G0VA 4U0CA 2QA4P 1M90Q 3G26A 4U0FA 2CWOA 3H47A 4GR2A 1VQPP 4PH1A 3G6EP 3CC2P 4XROA 1VQNP 3CD6P 3CMAP 2Z46A 3G21A 1A8OA 5HGNA 3G4SP 3DS5A 2QEXP 1RO0A 3MGEA 4U0DA 2PEIA 4IPYA 2M8PA 3OW2O 2PEOA 3CCEP 3VRLC 1AUMA 1VQKP 1W2BO 3HZQA 3P05A 2EG5A 2OARA 5F2KA 1N8RQ 2PENA 3B5IA 4XRQA 1NJIQ 3CCSP 3CC7P 2EFJA 1VQ4P 4U0EA 1YJWP 2M8LA 5F2OA 4XFZA 1VQ9P 4COPA 3HYBA 3I56P 1M74A 3CXCO 2M8NA 2XXMA 1KC8Q 4COCA 3Q20A 3G71P 3G28A 1KD1Q 2PEKA 3DS0A 3CC4P 1M6EX 3CCMP 1K8AQ 3M1MA 4WYMA 3DS1A 1K30A 1QVGO 3CCRP 2Z45A 5I4TG 4XFYA 1Q86Q 1IUQA 3CMEP 4M0IA
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 3DTJ A;  3DS4 A;  2XT1 A;  1EIA A;  3DS2 A;  3NTE A;  2ONT A;  1QRJ A;  4XRQ A;  4PH0 A;  1EOQ A;  5HGM A;  2BUO A;  3G0V A;  4U0C A;  3G26 A;  4U0E A;  3H47 A;  3DS3 A;  4U0F A;  4U0B A;  2M8L A;  4XFZ A;  5HGO A;  4PH1 A;  4XRO A;  4COP A;  1A43 A;  2LF4 A;  3G29 A;  2M8N A;  3G1G A;  2XXM A;  4COC A;  2JYG A;  3G21 A;  1BAJ A;  1A8O A;  2XV6 A;  3G28 A;  5HGN A;  3DS0 A;  3DS5 A;  2L6E A;  3G1I A;  3LRY A;  4U0A A;  5JPA A;  1D1D A;  3MGE A;  4U0D A;  4IPY A;  2JO0 A;  4QNB A;  2M8P A;  4WYM A;  3DS1 A;  5HGL A;  2EIA A;  3DPH A;  3H4E A;  3VRL C;  1AUM A;  5I4T G;  2KOD A;  4XFY A;  2JYL A;  4XFX A;  1E6J P;  3P05 A;  5DCK A;  4M0I A; 
#chains in the Genus database with same CATH topology
 2QNW A;  3WBH A;  2KGE A;  4HKG A;  3CCL P;  1EMV A;  2DNW A;  4U0A A;  4QNB A;  2LOL A;  5EJD A;  1UJZ A;  3DPH A;  4BPH A;  2BHV A;  2E1M A;  1MZ8 A;  2KGA A;  2EHT A;  1QRJ A;  2PEQ A;  4CA3 A;  2GYK A;  2LF4 A;  3G29 A;  2JYG A;  2LTE A;  2KR5 A;  2L6E A;  1RNI A;  3B4Q A;  4BPF A;  1Q81 Q;  4GR6 A;  3CCQ P;  1OR5 A;  1HQB A;  1S72 P;  1YJ9 P;  2N98 A;  4U0F A;  3CC2 P;  4XRO A;  3CMA P;  1ACP A;  1L0I A;  5HGN A;  1RO0 A;  5EW5 E;  1Z6M A;  4IPY A;  1VQK P;  3P05 A;  2EG5 A;  5F2K A;  2K0X A;  2PEN A;  3CCS P;  2N50 A;  3RG2 A;  2KGD A;  2L9F A;  2M8L A;  2ROQ A;  4XFZ A;  2JU1 A;  4COP A;  2M8N A;  4BPG A;  2VLP A;  1KD1 Q;  3CC4 P;  4NEO A;  2MR8 A;  1K30 A;  2MF4 A;  2Z45 A;  2JBG A;  5KP7 B;  2MD9 A;  3U43 A;  1FR2 A;  2CQ8 A;  2OTJ P;  2Z44 A;  3DS3 A;  1YJN P;  2DGY A;  3CCV P;  2K92 A;  2KW2 A;  1BXI A;  5KP6 B;  2WPT A;  2N5H A;  2KG9 A;  2GZE A;  1BAJ A;  3LRY A;  2JO0 A;  1QVF O;  2MY5 A;  5HGL A;  1ZMB A;  5HV8 A;  1E6J P;  1EIA A;  3DS2 A;  3CCJ P;  5F2N A;  3I55 P;  1NQ4 A;  2BUO A;  4PXH B;  5KP8 B;  5HGO A;  1K9M Q;  1VQ5 P;  3E2D A;  1AF8 A;  1GXH A;  2FHS C;  3EJE A;  3NY7 B;  1RO2 A;  3GZL A;  2FVA A;  2JYL A;  2X2B A;  3G0V A;  1VHN A;  2QA4 P;  2L0Q A;  4GR2 A;  2AFE A;  1VQN P;  4UHP B;  1A8O A;  3G4S P;  1VKU A;  3MGE A;  4U0D A;  2GDX A;  7CEI A;  3VRL C;  1W2B O;  3GKL C;  1N8R Q;  2GZI A;  4XRQ A;  1X3O A;  1CEI A;  2AVA A;  2CNR A;  1VQ9 P;  2LKI A;  3HYB A;  2KOO A;  2JAZ A;  3G28 A;  3EJD A;  1DNY A;  1K8A Q;  2L4B A;  5I4T G;  2PNG A;  4XFY A;  3CME P;  4M0I A;  1M1K Q;  2ONT A;  4H2X C;  1YHQ P;  2KOP A;  4DG9 A;  1A43 A;  2FQ0 A;  2NO8 A;  2KWL A;  1K73 Q;  2KG6 A;  4H2W C;  3CPW O;  1VQ6 P;  1VQM P;  1F80 D;  5DCK A;  2FQ2 A;  3DS4 A;  1T8K A;  2P9X A;  5HGM A;  1Q7Y Q;  2OTL P;  1VQO P;  1KQS O;  5BS1 A;  1YIJ P;  3G1G A;  1ZNV A;  2JQ4 A;  2XV6 A;  1D1D A;  1UNK A;  2KOR A;  2PY8 A;  2LML A;  5BS2 A;  5JPA A;  4PH0 A;  2CGQ A;  1M90 Q;  2VLN A;  3LMO A;  2CWO A;  3H47 A;  3CD6 P;  2FQ1 A;  2VLQ A;  2VLO A;  1IMP A;  3G21 A;  3DS5 A;  2QEX P;  3CE7 A;  4PWV B;  2M8P A;  3OW2 O;  3CCE P;  2AF8 A;  2K5X A;  2N5I A;  2OAR A;  5HVC A;  2K0D X;  3B5I A;  4IZ6 A;  2K94 A;  1VQ4 P;  1YJW P;  2KGC A;  3I56 P;  3CXC O;  2XXM A;  1KC8 Q;  2FVE A;  3DS0 A;  1M6E X;  2LL8 A;  2N6Y A;  2LPK A;  3M1M A;  2K93 A;  1QVG O;  3CCR P;  2LIU A;  1Q86 Q;  1IUQ A;  2JU2 A;  3DTJ A;  1YIT P;  1IMQ A;  4U0B A;  1VQ7 P;  1VQL P;  2KOQ A;  2JB0 A;  3G1I A;  1YI2 P;  3GJN A;  2EIA A;  3H4E A;  4XFX A;  2M5R A;  2L22 A;  3NTE A;  2KOS A;  2GDW A;  2GZJ A;  2N6Z A;  1M6N A;  3CCU P;  1JJ2 O;  2MVU A;  2XZ0 D;  2MR7 A;  1GXG A;  2PEJ A;  1Q82 Q;  3H0D A;  2GZG A;  1VQ8 P;  1HY8 A;  2KOD A;  2K2Q A;  2JGP A;  2XT1 A;  3RG6 C;  2EHS A;  2PEM A;  4R0M A;  1E0H A;  1EOQ A;  4U0C A;  3G26 A;  2CG5 B;  1DV5 A;  1VQP P;  4H2Y C;  1GPJ A;  4F37 A;  4PH1 A;  3G6E P;  3GZM A;  2Z46 A;  1AYI A;  2GZF A;  2ERH A;  2PEI A;  3EJB A;  2PEO A;  1AUM A;  3HZQ A;  2FAD A;  2XZ1 C;  1KLP A;  1NJI Q;  2FAC A;  2FAE A;  4QKO A;  3CC7 P;  2GDY A;  2EFJ A;  4U0E A;  2KG8 A;  5F2O A;  1M74 A;  2AFD A;  4COC A;  3Q20 A;  2VSQ A;  3G71 P;  2MVV A;  2PEK A;  3CCM P;  2K0Y A;  4MRT C;  5CZD B;  4WYM A;  3DS1 A;  1L0H A;  2LIW A;  2FVF A; 
#chains in the Genus database with same CATH homology
 3DTJ A;  1M1K Q;  2ONT A;  1YHQ P;  1YIT P;  3WBH A;  3CCL P;  2OTJ P;  2Z44 A;  4U0B A;  3DS3 A;  1YJN P;  2DGY A;  3CCV P;  1A43 A;  1VQ7 P;  1VQL P;  1BAJ A;  1K73 Q;  4U0A A;  3G1I A;  3LRY A;  1YI2 P;  3CPW O;  2JO0 A;  4QNB A;  1VQ6 P;  1QVF O;  1VQM P;  5HGL A;  2EIA A;  1ZMB A;  3DPH A;  3H4E A;  4XFX A;  1E6J P;  2BHV A;  5DCK A;  2E1M A;  3DS4 A;  1EIA A;  3DS2 A;  3NTE A;  1QRJ A;  2PEQ A;  3CCJ P;  5F2N A;  2P9X A;  5HGM A;  3I55 P;  2BUO A;  1Q7Y Q;  2OTL P;  5HGO A;  1K9M Q;  1VQO P;  1VQ5 P;  2LF4 A;  3E2D A;  5BS1 A;  1KQS O;  1M6N A;  3G1G A;  3G29 A;  3CCU P;  1YIJ P;  1JJ2 O;  2JYG A;  2XV6 A;  2L6E A;  1D1D A;  1RNI A;  1RO2 A;  1Q81 Q;  4GR6 A;  2PEJ A;  1Q82 Q;  2PY8 A;  5BS2 A;  3H0D A;  5JPA A;  3CCQ P;  1VQ8 P;  2KOD A;  2JYL A;  2XT1 A;  3RG6 C;  2PEM A;  4PH0 A;  1EOQ A;  1S72 P;  1YJ9 P;  3G0V A;  4U0C A;  2QA4 P;  1M90 Q;  3G26 A;  4U0F A;  2CWO A;  3H47 A;  4GR2 A;  1VQP P;  4PH1 A;  3G6E P;  3CC2 P;  4XRO A;  1VQN P;  3CD6 P;  3CMA P;  2Z46 A;  3G21 A;  1A8O A;  5HGN A;  3G4S P;  3DS5 A;  2QEX P;  1RO0 A;  3MGE A;  4U0D A;  2PEI A;  4IPY A;  2M8P A;  3OW2 O;  2PEO A;  3CCE P;  3VRL C;  1AUM A;  1VQK P;  1W2B O;  3HZQ A;  3P05 A;  2EG5 A;  2OAR A;  5F2K A;  1N8R Q;  2PEN A;  3B5I A;  4XRQ A;  1NJI Q;  3CCS P;  3CC7 P;  2EFJ A;  1VQ4 P;  4U0E A;  1YJW P;  2M8L A;  5F2O A;  4XFZ A;  1VQ9 P;  4COP A;  3HYB A;  3I56 P;  1M74 A;  3CXC O;  2M8N A;  2XXM A;  1KC8 Q;  4COC A;  3Q20 A;  3G71 P;  3G28 A;  1KD1 Q;  2PEK A;  3DS0 A;  3CC4 P;  1M6E X;  3CCM P;  1K8A Q;  3M1M A;  4WYM A;  3DS1 A;  1K30 A;  1QVG O;  3CCR P;  2Z45 A;  5I4T G;  4XFY A;  1Q86 Q;  1IUQ A;  3CME P;  4M0I 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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3DS5A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization